RetrogeneDB ID: retro_ecab_1128

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:100190973..100192142(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000005432
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSECAG00000023064
• Aliases: DCAF12, WDR40A
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_ecab_1128
CTGCGCGGCTACGCGGTGCAGAAGCTGCCCGAGCTGCTGCGGGAGCGCGAGCTGGCCCTGGGCACCCTCAACAAGGTGTT
CGCGTCGCAGTGGCTGAACGCCAGGCAGGTGGTGTGCGGCACCAAGTGCAACACGCTCTTCGTGGTGGACGTGCAGTCGG
GCCAGATCACGCGCATCCCCCTCATGCGGGACCGGGAACCCGGGCCGGCTCGGGCCCAGACGAGCTGCGGCATCCACGCC
ATCGAGTTGAATCCCTCCAAGACGCTTCTGGCCACGGGGGGCGAGAACCCCAACAGTCTGGCTGTCTACCAGCTGCCCAC
CCTGGACCCCGTGTGCCTGGGCGACCGCCTCGGCCACAGGGACTGGATCTTCGCCATCGCCTGGATGAGTGACACAGTGG
CTGTGAGCGGCTCCCGCGATGGCACCGTGGCTCTGTGGCGGATGGACCCCGACATATTCAATGGCAGCATCGCCTGGCAC
AACGACGCGGGGCTCCCCGTGTACGCCCACATCCGTCCAAGGGACTTGGAGACCATCCCCAGGGCCAGCACCAACCCCAG
TAACCGCAAGGTACGGGCCCTGGCCTTCAGTGGCAAGAACCAGGAGCTGGGAGCGGTGTCCCTGGACGGCTACTTCCACC
TGTGGAAAGCCCGGAGCACCCTGTCCAGGCTGCTGTCCATCAGGCTGCCCTACTGCCGAGAGAACGTGTGCCTAACCTAC
TGCGACGAGTTGTCCCTGTACGCGGTGGGCTCCCAGTCCCACGTCTCTTTCCTGGATCCCCGCCAGCGCCAGCAGAACAT
CACGGCCCCTGTGCTCTCGAGAGGGCGGCACGGGCGTGCGCTCGCTGAGCTTCTACCAGCACATCGTCACCGTGGGCACG
GGCCACGGCTCCCTGCTCTTCTATGACGTCAGAGCGCAGAAGTTCCTGGAAGGAGAAGGCCTTGGCCAGCCCGGACTCCT
CTCCCGGGCCCGCAGCGAGGAAGCTCAAGCTCACCTGTGGCAGAGGCTGGCTCAACCACGATGACCTGTGGGTGAACTAC
TTTGGCGGCGTAGGCGAGTTCCCCAACGCGCTCTACACCCACTGCTACAACTGGCCTGAGATGAAGCTCTTCGTGGCTGG
GGGCCCTCTCCCTTCAGGCCTCCATGGGAACTACGCAGGCCTCTGGAGC

Alignment

ORF - retro_ecab_1128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.05 %
• Parental protein coverage: 85.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LHGYAAQQLPGLLKEREFHLGTLNKVFASQWLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPGCV
          L.GYA.Q.LP.LL.ERE..LGTLNKVFASQWLN.RQVVCGTKCNTLFVVDVQ..QIT.IP...DREPG..
Retrocopy LRGYAVQKLPELLRERELALGTLNKVFASQWLNARQVVCGTKCNTLFVVDVQSGQITRIPLMRDREPGPA

Parental  -TQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGDD-GHKDWIFSIAWISDSMAVSGSRD
          ..Q..CGIHAIELNPS.TLLATGG.NPNSLA.Y.LPTLDPVC.GD..GH.DWIF.IAW.SD..AVSGSRD
Retrocopy RAQTSCGIHAIELNPSKTLLATGGENPNSLAVYQLPTLDPVCLGDRLGHRDWIFAIAWMSDTVAVSGSRD

Parental  GSMGLWEVTDDVLTKSDARHNVSRVPVYTHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDG
          G...LW....D....S.A.HN....PVY.HI....L..IP...TNP.N.KVRALAF..KN.ELGAVSLDG
Retrocopy GTVALWRMDPDIFNGSIAWHNDAGLPVYAHIRPRDLETIPRASTNPSNRKVRALAFSGKNQELGAVSLDG

Parental  YFHLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNV-KSVCSRERGSGI
          YFHLWKA..TLS.LLS..LPYCRENVCL.Y..E.S.YAVGSQ.HVSFLDPRQ...N.....CSRE.G.G.
Retrocopy YFHLWKARSTLSRLLSIRLPYCRENVCLTYCDELSLYAVGSQSHVSFLDPRQRQQNI>RPLCSREGGTGV

Parental  RSVSFYEHIITVGTGQGSLLFYDIRAQRFLE-ERLAACYGSKPKLAGENLKLTTGKGWLNHDETWRNYFS
          RS.SFY.HI.TVGTG.GSLLFYD.RAQ.FLE.E...A...S.P..A...LKLT.G.GWLNHD..W.NYF.
Retrocopy RSLSFYQHIVTVGTGHGSLLFYDVRAQKFLE>EKALASPDSSPGPAARKLKLTCGRGWLNHDDLWVNYFG

Parental  DIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
          ....FPNA.YTHCY.....KLFVAGGPLPSGLHGNYAGLWS
Retrocopy GVGEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGNYAGLWS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	33.71 RPM
SRP021940_cerebellum	0.57 RPM	26.07 RPM
SRP021940_embryo	0.33 RPM	40.79 RPM
SRP021940_placental_villous	0.00 RPM	44.02 RPM
SRP021940_synovial_membrane	0.14 RPM	39.64 RPM
SRP021940_testis	8.63 RPM	189.78 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1128 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1128 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1794
Sus scrofa	retro_sscr_17

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000309	1 retrocopy	retro_amel_73,
Bos taurus	ENSBTAG00000021573	3 retrocopies	retro_btau_1794, retro_btau_1795, retro_btau_1796,
Equus caballus	ENSECAG00000023064	2 retrocopies	retro_ecab_1128 , retro_ecab_1129,
Erinaceus europaeus	ENSEEUG00000013279	1 retrocopy	retro_eeur_403,
Microcebus murinus	ENSMICG00000005881	1 retrocopy	retro_mmur_14,
Macaca mulatta	ENSMMUG00000017458	1 retrocopy	retro_mmul_202,
Nomascus leucogenys	ENSNLEG00000004996	1 retrocopy	retro_nleu_6,
Otolemur garnettii	ENSOGAG00000015799	1 retrocopy	retro_ogar_237,
Ochotona princeps	ENSOPRG00000001281	2 retrocopies	retro_opri_1178, retro_opri_470,
Pongo abelii	ENSPPYG00000019127	1 retrocopy	retro_pabe_64,
Pteropus vampyrus	ENSPVAG00000008654	1 retrocopy	retro_pvam_16,
Sus scrofa	ENSSSCG00000010986	1 retrocopy	retro_sscr_17,
Ictidomys tridecemlineatus	ENSSTOG00000006904	1 retrocopy	retro_itri_168,
Tarsius syrichta	ENSTSYG00000014394	1 retrocopy	retro_tsyr_1965,
Tursiops truncatus	ENSTTRG00000010591	1 retrocopy	retro_ttru_8,